Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
|
com.compomics.util.experiment.identification.protein_sequences |
Protein sequence handling related classes.
|
Modifier and Type | Method and Description |
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ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
|
void |
Peptide.mapParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Maps the peptides to the proteins in the sequence database loaded in the
sequence factory.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Validates a peptide depending on its protein inference status.
|
Modifier and Type | Class and Description |
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class |
FMIndex
The FM index.
|
Modifier and Type | Class and Description |
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class |
ProteinTree
This class sorts the proteins into groups.
|
Modifier and Type | Method and Description |
---|---|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper()
Returns the default peptide mapper.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress,
int nThreads)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
int nThreads,
IdentificationParameters identificationParameters)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
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